No you haven't damaged it. I think that is just the antireflection coatings smearing slightly when rubbed.

Microfibre cloth, some lens cleaner and a hurricane blower should do the trick. I had this happen on my Sony A7r which is the same sensor as D800. I also got concerned but Ive cleaned optics many times and I knew the coatings can sometimes smear like that. It will even out with some cleaner and mircofibre cloth.

I continued to rub mine down making sure there was no trapped grit that could scratch. It evened out pretty well. Not 100% yet but thats not with cleaing fluid yet. I see no effect in the images though.